NM_024426.6(WT1):c.813G>C (p.Pro271=) AND Wilms tumor 1

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Feb 24, 2023
Review status:: criteria provided, conflicting classifications

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001107285.7

Allele description [Variation Report for NM_024426.6(WT1):c.813G>C (p.Pro271=)]

NM_024426.6(WT1):c.813G>C (p.Pro271=)

Gene:

WT1:WT1 transcription factor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_024426.6(WT1):c.813G>C (p.Pro271=)

HGVS:

NC_000011.10:g.32428030C>G
NG_009272.1:g.12512G>C
NG_122166.1:g.213C>G
NM_000378.6:c.813G>C
NM_001198551.2:c.162G>C
NM_001198552.2:c.162G>C
NM_001407044.1:c.813G>C
NM_001407045.1:c.813G>C
NM_001407046.1:c.813G>C
NM_001407047.1:c.690G>C
NM_001407048.1:c.813G>C
NM_001407049.1:c.813G>C
NM_001407050.1:c.690G>C
NM_001407051.1:c.51G>C
NM_024424.5:c.813G>C
NM_024425.2:c.798G>C
NM_024426.6:c.813G>CMANE SELECT
NP_000369.4:p.Pro271=
NP_001185480.1:p.Pro54=
NP_001185480.1:p.Pro54=
NP_001185481.1:p.Pro54=
NP_001393973.1:p.Pro271=
NP_001393974.1:p.Pro271=
NP_001393975.1:p.Pro271=
NP_001393976.1:p.Pro230=
NP_001393977.1:p.Pro271=
NP_001393978.1:p.Pro271=
NP_001393979.1:p.Pro230=
NP_001393980.1:p.Pro17=
NP_077742.3:p.Pro271=
NP_077743.2:p.Pro266=
NP_077744.3:p.Pro266=
NP_077744.4:p.Pro271=
LRG_525t1:c.798G>C
LRG_525t2:c.162G>C
LRG_525:g.12512G>C
LRG_525p1:p.Pro266=
LRG_525p2:p.Pro54=
NC_000011.9:g.32449576C>G
NM_001198551.1:c.162G>C
NM_024426.3:c.798G>C
NM_024426.4:c.798G>C
NR_160306.1:n.992G>C
NR_176266.1:n.992G>C

Links:

dbSNP: rs1341857958

NCBI 1000 Genomes Browser:

rs1341857958

Molecular consequence:

NR_160306.1:n.992G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176266.1:n.992G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000378.6:c.813G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001198551.2:c.162G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001198552.2:c.162G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407044.1:c.813G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407045.1:c.813G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407046.1:c.813G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407047.1:c.690G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407048.1:c.813G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407049.1:c.813G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407050.1:c.690G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407051.1:c.51G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_024424.5:c.813G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_024425.2:c.798G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_024426.6:c.813G>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Name:: Wilms tumor 1 (WT1)
Synonyms:: Wilms tumor, somatic
Identifiers:: MONDO: MONDO:0008679; MedGen: CN033288; Orphanet: 654; OMIM: 194070

Recent activity

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Saccharomyces cerevisiae strain XXYS1.4 genome assembly, chromosome: 12
Saccharomyces cerevisiae strain XXYS1.4 genome assembly, chromosome: 12
gi|1932845190|emb|LR813613.2|

Nucleotide
VEGFC [Homo sapiens]
VEGFC [Homo sapiens]
gi|49456749|emb|CAG46695.1|

Protein
ATP synthase subunit I [Psychrosphaera saromensis]
ATP synthase subunit I [Psychrosphaera saromensis]
gi|1353613765|ref|WP_105051297.1|

Protein
DUF6559 family protein [Psychrosphaera saromensis]
DUF6559 family protein [Psychrosphaera saromensis]
gi|2573577667|ref|WP_308428109.1|

Protein
AmpG family muropeptide MFS transporter [Psychrosphaera saromensis]
AmpG family muropeptide MFS transporter [Psychrosphaera saromensis]
gi|2075723746|ref|WP_219846457.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001264426	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 28, 2017)	germline	clinical testing	Citation Link,
SCV004815809	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Feb 24, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001264426

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 28, 2017)

germline

clinical testing

Citation Link,

SCV004815809

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely Benign
(Feb 24, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	2	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001264426.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From All of Us Research Program, National Institutes of Health, SCV004815809.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		2	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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